Hi. I am trying to make sense of a previously written DESeq analysis which uses the “name” parameter to obtain results. A sample code is below, the first two lines are straightforward - making the Input file and running DESeq. My question is what does the results function return when the name parameter points to only a single condition. What is the comparison that is made? Thanks in advance for the input and I will also appreciate if you can point out the documentation regarding this usage.
ddsInput <- DESeqDataSetFromMatrix(countdata, coldata, ~ condition)
dds <- DESeq(ddsInput, betaPrior=TRUE, modelMatrixType="expanded")
myresults <- results(dds, name = “condition1”)